Article
Chemistry, Physical
Agnieszka G. Lipska, Adam K. Sieradzan, Su''meyye Atmaca, Cezary Czaplewski, Adam Liwo
Summary: A reliable representation of local interactions is crucial for accurate protein structure and dynamics modeling. Traditional approaches mainly focus on parameterizing preset formulas rather than physics-based derivation. Recent advancements suggest the consideration of virtual bond angles and multiple torsional terms. Furthermore, separating residue-based torsional potentials into regular and improper potentials is a new approach.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Emilia A. Lubecka, Adam Liwo
Summary: The ESCASA algorithm was implemented to estimate proton positions from coarse-grained geometry in protein structure modeling. The method utilizes a penalty function and Hamiltonian replica exchange molecular dynamics for handling ambiguous distance restraints and conducting conformational search. The results show that the method can generate high-quality models for flexible protein structures.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Emily Hendrix, Stefano Motta, Robert F. Gahl, Yi He
Summary: The unfolded state of proteins presents challenges in understanding their structural basis. Recent experiments on the folding of a ribonuclease homologue identified regions involved in the initial folding. This study used molecular dynamics simulations to confirm the experimentally observed structures and identified key folding initiation sites. Self-organization map analysis further revealed important structural states in the early folding events.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
YongZhi Wang, Yaoyao Xue, Qiang Lei, Jiawei Yang, Yuhua Xue, Shuling Shen, Zhihong Tang, Junhe Yang
Summary: In this study, a three-dimensional self-crumpled carbon nanoarchitectonics was synthesized by GO-assisted carbonization. GO served as both a template and a catalyst for the carbonization reaction. The GLC reacted with GO under high temperature and acidic environment, resulting in the production of 5-HMF and the subsequent polymerization and carbonization into a two-dimensional carbon along GO sheets. GO provided nucleation sites and template for the directional polymerization and carbonization of GLC. The addition of GO reduced the activation energy of GLC polymerization and transformed the composite into a three-dimensional crumpled structure. The resulting CG-50 exhibited good electrocatalytic performance.
JOURNAL OF ALLOYS AND COMPOUNDS
(2022)
Article
Biochemical Research Methods
Masaki Tagashira, Kiyoshi Asai
Summary: By detecting homology among RNAs, probabilistic consideration of RNA structural alignments has improved the prediction accuracy of significant RNA prediction problems. ConsAlifold, a dynamic programming-based method, considers RNA structural alignments and achieves moderate running time and the best prediction accuracy of RNA consensus secondary structures among available prediction methods.
Article
Computer Science, Information Systems
Mingyang Song, Chunlin Li, Jingsong Ye, Xunqiang Gong, Youlong Luo
Summary: This paper proposes an improved DPoS-based consensus mechanism to address the issues of low decentralization, low motivation for node voting, and malicious behavior in the traditional DPoS consensus mechanism for blockchain-based UAV-assisted mobile edge computing. The study provides a framework for a blockchain-based UAV-assisted mobile edge computing system and analyzes the consensus mechanism design problem. It establishes a proxy node selection model based on blockchain node rights and votes and classifies node behaviors into positive and malicious behaviors to reward and punish reputation value. Experimental results demonstrate that the proposed algorithms can enhance network throughput, reduce block-out delay, and increase the proportion of secure proxy nodes.
COMPUTER COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Chen Jia, Libo Zhao, Min Li, Mingzhi Yu, Guoxi Luo, Nan Zhu, Xiangguang Han, Yong Xia, Ping Yang, Jiuhong Wang, Zhuangde Jiang
Summary: A novel structure of a MEMS piezoresistive accelerometer was proposed to improve sensitivity by using tiny piezoresistive beams (TPBs) to generate stress concentration region (SCR) and microleverage mechanism to amplify force. Model analyses and simulations were conducted to study the force amplification factor and its dependence on dimensional parameters. Three prototypes were fabricated and tested, and the results showed that the higher amplification factor led to higher sensitivity and better comprehensive performance.
IEEE SENSORS JOURNAL
(2023)
Article
Biochemical Research Methods
Anna Antoniak, Iga Biskupek, Krzysztof K. Bojarski, Cezary Czaplewski, Artur Gieldon, Mateusz Kogut, Malgorzata M. Kogut, Pawel Krupa, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Mateusz Marcisz, Martyna Maszota-Zieleniak, Sergey A. Samsonov, Adam K. Sieradzan, Magdalena J. Slusarz, Rafal Slusarz, Patryk A. Wesolowski, Karolina Zieba
Summary: The UNited RESidue (UNRES) force field was tested in CASP14, with improved GDT_TS scores in all three prediction modes compared to CASP13. Incorporating template assistance resulted in better predictions for UNRES models.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Acoustics
Florian Lacaze, Ahmad Paknejad, Didier Remond, Simon Chesne
Summary: This study examines the effectiveness of an integral force feedback controller in improving the damping of lightweight flexible structures. The control system parameters are tuned using both maximum damping and H-infinity optimization approaches. Two modifications to the integral force feedback are proposed to compensate for the soft stiffness and enhance the actuator's authority. By incorporating feedback terms, higher damping values can be achieved. The study also discusses optimal tuning, required actuator force, and stability based on an academic model of a single-degree-of-freedom cable structure.
JOURNAL OF VIBRATION AND CONTROL
(2022)
Article
Chemistry, Multidisciplinary
Chuang Yang, Xin Wu, Heyi Xia, Jingzhuo Zhou, Yifan Wu, Rui Yang, Guangmin Zhou, Ling Qiu
Summary: A 3D printed template-assisted method is used to fabricate additive-free 3D architected MXene aerogels with controllable structures and high performance. The MXene ink with a wide range of concentrations allows for the production of MXene aerogels with high structural freedom and fine feature size.
Article
Biophysics
Li Zhou, Xunxun Wang, Shixiong Yu, Ya-Lan Tan, Zhi-Jie Tan
Summary: Prediction of RNA three-dimensional structures is crucial for understanding the important biological functions of RNA. This study proposes a new model, FebRNA, based on fragment assembly, which consistently gives reliable predictions for different types of RNA structures.
BIOPHYSICAL JOURNAL
(2022)
Article
Pharmacology & Pharmacy
Cristina Garcia-Mouton, Mercedes Echaide, Luis A. Serrano, Guillermo Orellana, Fabrizio Salomone, Francesca Ricci, Barbara Pioselli, Davide Amidani, Antonio Cruz, Jesus Perez-Gil
Summary: Pulmonary surfactant (PS) is a potential drug delivery vehicle for inhaled therapies. The study investigated the contribution of surface-associated structures to the spreading of PS and the transport of drugs. The results showed that three-dimensional structures connected to the surfactant interfacial film can significantly enhance interfacial delivery.
Article
Engineering, Electrical & Electronic
Ian Waters, Lefan Wang, Dominic Jones, Ali Alazmani, Peter Culmer
Summary: The limited grasping control in Robot Assisted Surgery is a significant limitation. Researchers propose an alternative approach based on detecting localized slips caused by elastic properties of soft tissues. They design a sensor to detect incipient slip by monitoring the relative difference in tissue movement at the front and back of the grasper.
IEEE SENSORS JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Buse Bulut Kopuklu, Aurora Gomez-Martin, Martin Winter, Tobias Placke, Richard Schmuch, Selmiye Alkan Gursel, Alp Yurum
Summary: In this study, a sacrificial carbon fiber template was used to synthesize LiNi0.8Co0.15Al0.05O2 (C-NCA) cathode material, which exhibited high reversible capacity and stability suitable for high-rate and high-temperature battery operation. The anisotropic primary particle morphology with interconnected microstructure played a key role in improving ion transport and structural stability, outperforming the reference bare NCA material.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Engineering, Electrical & Electronic
Jun Liu, Zihui Gao, Zhaoqian Sun, Tao Jian, Weijian Liu
Summary: This paper proposes a radar adaptive detection architecture with an interference covariance matrix structure classifier and a bank of adaptive radar detectors. The architecture improves the estimation of the covariance matrix and the detection performance, especially with a small volume of training samples. Therefore, the newly proposed architecture can guarantee excellent detection performance for a wider class of operating scenarios.
DIGITAL SIGNAL PROCESSING
(2022)
Article
Chemistry, Multidisciplinary
Lukasz Golon, Adam K. K. Sieradzan
Summary: Nucleic acids are essential cellular components that have been studied using both experimental and theoretical approaches. Coarse-grain modeling, such as the NARES-2P model, allows for the study of nucleic acids on a longer time scale. This article presents a new software that reconstructs atomistic details from the NARES-2P model, which has been successfully applied to study various nucleic acid structures and behaviors.
Article
Chemistry, Multidisciplinary
Adam K. Sieradzan, Jordi Sans-Duno, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo, Henryk Leszczyfiski
Summary: The UNRES package for coarse-grained simulations of proteins has been significantly improved with algorithmic advancements, including optimized computations, reduced memory requirements, improved parallel performance, and capability to simulate large protein systems with high efficiency.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Marta Pagielska, Sergey A. Samsonov
Summary: Glycosaminoglycans (GAGs) are linear anionic polysaccharides that interact with proteins in the extracellular matrix and play important roles in cell signaling, tissue regeneration, and diseases such as cancer, Alzheimer's, and Parkinson's. This study investigates the structural and dynamic properties of chondroitin sulfates-4,6 (CS4, CS6) and dermatan sulfate (DS), revealing substantial differences between these GAGs. Understanding these differences can have practical implications for designing GAG-based drugs in regenerative medicine.
Article
Biochemical Research Methods
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
Summary: The UNRES-GPU package has been implemented on GPUs and achieved significant speed-up for large protein systems. It is capable of simulating large protein systems at the millisecond time scale.
Article
Chemistry, Multidisciplinary
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
Summary: The dynamics of HuNoV VLPs from GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains were investigated using long-time molecular dynamics simulations. The bending motion at the junction between the P1 and P2 subdomains of the major VP1 protein was found to be the main motion of the VLP units. The GII.2 strain exhibited more pronounced fluctuations and a greater angle with the VLP surface, which may explain its inability to bind HBGAs.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Malgorzata Graul, Natalia Karska, Magda Wachalska, Pawel Krupa, Magdalena J. Slusarz, Marcin Lubocki, Krystyna Bienkowska-Szewczyk, Sylwia Rodziewicz-Motowidlo, Adam K. Sieradzan, Andrea D. Lipinska
Summary: Proline residues, in particular the 52PPQ54 residues, play a crucial role in controlling the structure and function of proteins, especially in the N-terminal domain of the UL49.5 protein encoded by bovine herpesvirus 1. The proline hinge motif serves as an anchor into the membrane and is responsible for the structural and dynamic behavior of the protein, affecting its interaction with TAP and inhibition of its activity.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Ankur Gupta, Pawel Krupa, Oskar Engberg, Magdalena Krupa, Ankur Chaudhary, Mai Suan Li, Daniel Huster, Sudipta Maiti
Summary: Nature confines high concentrations of amphiphilic neurotransmitters like serotonin in synaptic vesicles, which affect the mechanical properties of lipid bilayer membranes. However, a mixture of specific lipids in natural vesicles, mimicking their ratios, is minimally perturbed by serotonin, suggesting an emergent mechanical property of these lipids. The role of cholesterol in dictating the mechanical perturbations is minor, indicating that nature utilizes a specific lipid mixture's vulnerability to serotonin to appropriately respond to physiological levels.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Adam Liwo, Maciej Pyrka, Cezary Czaplewski, Xubiao Peng, Antti J. Niemi
Summary: In this study, the long-term dynamics of three molecular motors were investigated using molecular dynamics simulations. The results show that rotational motion can occur with zero total angular momentum in both the microcanonical and canonical ensembles, and thermal motions can be converted into net rotation. These findings highlight the importance of molecular motors in facilitating movement and transportation within living organisms.
Article
Biochemistry & Molecular Biology
Pawel Krupa, Giovanni La Penna, Mai Suan Li
Summary: Charge polarization at the membrane interface is an important process in biology. This study investigates the effects of divalent cations and their association with lipid molecules, as well as the role of amyloid-beta 1-42 (A beta 42) peptides in ion homeostasis and lipid membrane protection. The results provide insights into the possible mechanisms of synaptic plasticity and the storage of divalent cations away from lipids by A beta 42 oligomers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Annemarie Danielsson, Sergey. A. A. Samsonov, Adam Liwo, Adam. K. K. Sieradzan
Summary: Heparin is a negatively charged unbranched polysaccharide involved in important biological processes. This study extends the UNICORN model to heparin and accurately predicts its conformation using the SUGRES-1P force field.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Natalia Karska, Igor Zhukov, Andrea D. Lipinska, Sylwia Rodziewicz-Motowidlo, Pawel Krupa
Summary: The UL49.5 protein encoded by HSV-1 has a unique structure with a flexible extracellular N-terminus, a long transmembrane alpha-helix, and a short unordered C-terminus, unlike the homologs from other herpesviruses. This structural information sheds light on the lack of biological activity of UL49.5 in inhibiting the TAP-dependent antigen presentation pathway.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2023)
Article
Chemistry, Physical
Christian Schulze, Annemarie Danielsson, Adam Liwo, Daniel Huster, Sergey A. Samsonov, Anja Penk
Summary: This study compares the binding of highly charged heparin with peptides of varying charge density to the regulatory protein IL-8. The results demonstrate that the peptide ligands have weaker binding affinity to IL-8 compared to GAGs. Molecular simulations suggest that the entropic loss of peptides might account for this difference.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Christian Schulze, Annemarie Danielsson, Adam Liwo, Daniel Huster, Sergey A. Samsonov, Anja Penk
Summary: This study investigates the binding process between proteins and glycosaminoglycans (GAGs) from the extracellular matrix and compares the binding affinity of highly charged heparin (HP) hexasaccharide and negatively charged peptides with different charge densities. The results suggest that the difference in binding affinity between GAGs and peptides may be attributed to the entropic loss of peptides during binding.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)